Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold505
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 53672
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:5644 original size:161 final size:160
Alignment explanation
Indices: 4544--6009 Score: 1016
Period size: 161 Copynumber: 9.1 Consensus size: 160
4534 CATAAATTAC
* * * * * * * *
4544 AAGTATTG-TAAAAGATACATAATTTGAAAA-CCAATTTGCATATTAAAATAAATACAAAATAAG
1 AAGTATCGTTAAAAGATATATAATTCGAAAATCC-TTTTACTTATTAAAACAAAAACAAAATAAG
* * * *
4607 TATTTATAATAAAATACG-GGTTTAGGTATAGTAAAAGGTGTATGATTTCAATAACCAAAG-AAA
65 ---CTATAATAAAATA-GAGGTTTAGGTATAGTGAAAGGTGTATGATTCCGATAACCAAAGCAAA
* * *
4670 ATAAGCATTTATA-AGACACGAT-GGAGTATAGA-TTT
126 ATAAGCATTTATATA-ACA--ATCGAAATATAAACTTT
* * * *
4705 -AGTCATCGTTAAAAGATATATAATTTGAAAA-CCATCTTACTTA--ATAATAAAAACAAAATAA
1 AAGT-ATCGTTAAAAGATATATAATTCGAAAATCC-TTTTACTTATTAAAACAAAAACAAAATAA
* * * * * * * *
4766 GCATTTATAATAAAATACAAGTTTAAGTATAATAAAAGATGTATGATTCCGATAACGAAAGCGAA
64 GC---TATAATAAAATAGAGGTTTAGGTATAGTGAAAGGTGTATGATTCCGATAACCAAAGCAAA
* * *
4831 ATAAGAATTTATAAAACACGAT-GGAATATAAACTTT
126 ATAAGCATTTATATAACA--ATCGAAATATAAACTTT
4867 AAGTATCGTTAAAAGATATATAAATT-GAAAA-CCATTTTACTTATTAAAACAAAAACAAAATAA
1 AAGTATCGTTAAAAGATATAT-AATTCGAAAATCC-TTTTACTTATTAAAACAAAAACAAAATAA
* * ** * * *
4930 GCATTTATAATAAAATATAAGTTTAGGTATAGAAAAAAGTGTACGATTCCGATAACGAAAGCAAA
64 GC---TATAATAAAATAGAGGTTTAGGTATAGTGAAAGGTGTATGATTCCGATAACCAAAGCAAA
* * *
4995 ATAAGTATTTATAGAACACAAT-GGAATATAAACTTT
126 ATAAGCATTTATA-TA-ACAATCGAAATATAAACTTT
* * * ** *
5031 AGGTATCGTTAAAAGATATATAATTTG-AAA-CCATTTTGCTTATTAAAACAGGAACAAAATAAT
1 AAGTATCGTTAAAAGATATATAATTCGAAAATCC-TTTTACTTATTAAAACAAAAACAAAATAAG
* * * * ** * * * *
5094 CATTTATAATAAAATACAAGTTTAGGTATTGTAAAAGAAGTA--A----AATAAGCATTTA-TAA
65 C---TATAATAAAATAGAGGTTTAGGTATAGTGAAAGGTGTATGATTCCGATAACCA--AAGCAA
** * ** * ** *
5152 CGTACG-ATGAAATATAA-ACTTTAAATAT---CGTTAA
125 AATAAGCAT-TTATATAACAATCGAAATATAAAC-TT-T
* *** * * * *
5186 AAGATAT--ATAATTCAT-TATAATTCAAAAATCATTATACTTATTAAAATAAAAACAAAAGTAA
1 AAG-TATCGTTAAAAGATATATAATTCGAAAATCCTTTTACTTATTAAAACAAAAACAAAA-TAA
* * *
5248 GCATCTATAATAAAATAGAGGTTTAGGTATAGTGAAAGGTGGATGATTCCGATAACGAAAGAAAA
64 G---CTATAATAAAATAGAGGTTTAGGTATAGTGAAAGGTGTATGATTCCGATAACCAAAGCAAA
5313 ATTAA-CATTTATAGTACACAAT-GAAATATAAACTTT
126 A-TAAGCATTTATA-TA-ACAATCGAAATATAAACTTT
* * *
5349 AATTAGTATCGTTAAAAGATATATAATTCGAAAA-CCGTCTTACTTATTAAAATAGAAACAAAAT
1 -A--AGTATCGTTAAAAGATATATAATTCGAAAATCC-TTTTACTTATTAAAACAAAAACAAAAT
* * * * *
5413 AAGCATTTATAATAAAATAAAGGTTTAGGTATTGCGGAAGGTGTATGATTCCTATAACCAAAGCA
62 AAGC---TATAATAAAATAGAGGTTTAGGTATAGTGAAAGGTGTATGATTCCGATAACCAAAGCA
* *
5478 AAATAAGTATTTATATAACACTCGTAAAATATAAACTTT
124 AAATAAGCATTTATATAACAATCG--AAATATAAACTTT
* * *
5517 AAGTATCGTTAAAAGATATCTAATTTGAAAA-CCTATTTACTTATTGAAACAAAAACAAAATAAG
1 AAGTATCGTTAAAAGATATATAATTCGAAAATCCT-TTTACTTATTAAAACAAAAACAAAATAAG
*
5581 C-ATAATAAAATAGAGGTTTAGGTATAGTGAAAGGTGTATGATTCCGATAACCAAAGAAAAATAA
65 CTATAATAAAATAGAGGTTTAGGTATAGTGAAAGGTGTATGATTCCGATAACCAAAGCAAAATAA
* *
5645 GCATTTATATAAC-ATC--CAT-GAAA---T
130 GCATTTATATAACAATCGAAATATAAACTTT
* * *
5669 -A-TATCGTTAAAAGATATATAATTCGAAAATCGTTTTACTTATTAAAACAAAAACAAATTACGC
1 AAGTATCGTTAAAAGATATATAATTCGAAAATCCTTTTACTTATTAAAACAAAAACAAAATAAGC
* * * *
5732 ATTTATAACAAAATAGAGGTATAGATATGGTGAAAGGTGTATGATTCCGATAACCAAAGCAAAAT
66 ---TATAATAAAATAGAGGTTTAGGTATAGTGAAAGGTGTATGATTCCGATAACCAAAGCAAAAT
* *
5797 AAGCATTTATAATATATAAT-GAAATATAAATTTT
128 AAGCATTTAT-ATA-ACAATCGAAATATAAACTTT
* * * * *
5831 AAGTATCGTTAAAAGATATATAATTCGAAAATCGTTCTACTTATT--AA-AAAAATAAAGTACGC
1 AAGTATCGTTAAAAGATATATAATTCGAAAATCCTTTTACTTATTAAAACAAAAACAAAATAAGC
* * * *
5893 ATTTATAATAAAATAGAGGTATAGGTATGGTGAAAGGTGTATGATTCTGATAACCAAAGCAAAAC
66 ---TATAATAAAATAGAGGTTTAGGTATAGTGAAAGGTGTATGATTCCGATAACCAAAGCAAAAT
* *
5958 AAGCATTTATATAACACTCATAAAATATAAACTTT
128 AAGCATTTATATAACAATC--GAAATATAAACTTT
* * *
5993 AAGCATAGTTGAAAGAT
1 AAGTATCGTTAAAAGAT
6010 GTAGTTTAGG
Statistics
Matches: 1071, Mismatches: 156, Indels: 155
0.77 0.11 0.11
Matches are distributed among these distances:
150 53 0.05
151 3 0.00
152 1 0.00
153 8 0.01
154 97 0.09
155 45 0.04
156 12 0.01
157 11 0.01
158 11 0.01
159 8 0.01
160 77 0.07
161 197 0.18
162 102 0.10
163 82 0.08
164 168 0.16
165 66 0.06
166 11 0.01
167 71 0.07
168 48 0.04
ACGTcount: A:0.48, C:0.09, G:0.13, T:0.30
Consensus pattern (160 bp):
AAGTATCGTTAAAAGATATATAATTCGAAAATCCTTTTACTTATTAAAACAAAAACAAAATAAGC
TATAATAAAATAGAGGTTTAGGTATAGTGAAAGGTGTATGATTCCGATAACCAAAGCAAAATAAG
CATTTATATAACAATCGAAATATAAACTTT
Found at i:5928 original size:315 final size:313
Alignment explanation
Indices: 5355--5986 Score: 853
Period size: 315 Copynumber: 2.0 Consensus size: 313
5345 CTTTAATTAG
* *
5355 TATCGTTAAAAGATATATAATTCGAAAACCGTCTTACTTATTAAAATAGAAACAAAATAAGCATT
1 TATCGTTAAAAGATATATAATTCGAAAACCGTCTTACTTATTAAAACAAAAACAAAATAAGCATT
* * * * * *
5420 TATAATAAAATAAAGGTTTAGGTATTGCGGAAGGTGTATGATTCCTATAACCAAAGCAAAATAAG
66 TATAACAAAATAAAGGTATAGATATGGCGAAAGGTGTATGATTCCGATAACCAAAGCAAAATAAG
* * * *
5485 TATTTATATAACACTCGTAAAATATAAACTTTAAGTATCGTTAAAAGATATCTAATTTGAAAACC
131 CATTTATATAACAATCG-AAAATATAAACTTTAAGTATCGTTAAAAGATATATAATTCGAAAACC
* *
5550 TATTTACTTATTGAAACAAAAACAAAATAAGCATAATAAAATAGAGGTTTAGGTATAGTGAAAGG
195 TATCTACTTATT-AAACAAAAACAAAATAAGCATAATAAAATAGAGGTATAGGTATAGTGAAAGG
* *
5615 TGTATGATTCCGATAACCAAAGAAAAATAAGCATTTATATAACA-TCCATGAAATA
259 TGTATGATTCCGATAACCAAAGAAAAACAAGCATTTATATAACACT-CATAAAATA
* * * *
5670 TATCGTTAAAAGATATATAATTCGAAAATCGTTTTACTTATTAAAACAAAAACAAATTACGCATT
1 TATCGTTAAAAGATATATAATTCGAAAACCGTCTTACTTATTAAAACAAAAACAAAATAAGCATT
* *
5735 TATAACAAAATAGAGGTATAGATATGGTGAAAGGTGTATGATTCCGATAACCAAAGCAAAATAAG
66 TATAACAAAATAAAGGTATAGATATGGCGAAAGGTGTATGATTCCGATAACCAAAGCAAAATAAG
* *
5800 CATTTATAATATATAAT-G-AAATATAAATTTTAAGTATCGTTAAAAGATATATAATTCGAAAAT
131 CATTTAT-ATA-ACAATCGAAAATATAAACTTTAAGTATCGTTAAAAGATATATAATTCGAAAA-
* * * * *
5863 CGT-TCTACTTATT-AA-AAAAATAAAGTACGCATTTATAATAAAATAGAGGTATAGGTATGGTG
193 CCTATCTACTTATTAAACAAAAACAAAATAAGC----ATAATAAAATAGAGGTATAGGTATAGTG
* *
5925 AAAGGTGTATGATTCTGATAACCAAAGCAAAACAAGCATTTATATAACACTCATAAAATA
254 AAAGGTGTATGATTCCGATAACCAAAGAAAAACAAGCATTTATATAACACTCATAAAATA
5985 TA
1 TA
5987 AACTTTAAGC
Statistics
Matches: 278, Mismatches: 31, Indels: 16
0.86 0.10 0.05
Matches are distributed among these distances:
311 12 0.04
312 2 0.01
314 50 0.18
315 206 0.74
316 5 0.02
317 3 0.01
ACGTcount: A:0.46, C:0.10, G:0.13, T:0.30
Consensus pattern (313 bp):
TATCGTTAAAAGATATATAATTCGAAAACCGTCTTACTTATTAAAACAAAAACAAAATAAGCATT
TATAACAAAATAAAGGTATAGATATGGCGAAAGGTGTATGATTCCGATAACCAAAGCAAAATAAG
CATTTATATAACAATCGAAAATATAAACTTTAAGTATCGTTAAAAGATATATAATTCGAAAACCT
ATCTACTTATTAAACAAAAACAAAATAAGCATAATAAAATAGAGGTATAGGTATAGTGAAAGGTG
TATGATTCCGATAACCAAAGAAAAACAAGCATTTATATAACACTCATAAAATA
Found at i:6244 original size:29 final size:29
Alignment explanation
Indices: 6202--6260 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
6192 CTAACCAGAA
6202 AGTAAAAGAGGTAGTGAAATTAAATGCTT
1 AGTAAAAGAGGTAGTGAAATTAAATGCTT
6231 AGTAAAAGAGGTAGTGAAATTAAATGCTT
1 AGTAAAAGAGGTAGTGAAATTAAATGCTT
6260 A
1 A
6261 CCAAGAGATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.46, C:0.03, G:0.24, T:0.27
Consensus pattern (29 bp):
AGTAAAAGAGGTAGTGAAATTAAATGCTT
Found at i:12974 original size:41 final size:40
Alignment explanation
Indices: 12872--13029 Score: 190
Period size: 40 Copynumber: 3.9 Consensus size: 40
12862 CGTTTGTGGA
* * *
12872 AAAAAACGCTGCTATTGCTTTACCTTTAACGGCGTTTATG
1 AAAAAATGCCGCTATTGCTTTACCTTTTACGGCGTTTATG
* *
12912 AAAAAATGCCGCTGTTGCTTTACCTTTTGCGGCGTTTATG
1 AAAAAATGCCGCTATTGCTTTACCTTTTACGGCGTTTATG
* * * *
12952 AGAAAAATGCCACTATTACTTTACTTTTTACGGCGTTTACG
1 A-AAAAATGCCGCTATTGCTTTACCTTTTACGGCGTTTATG
* * * *
12993 CAAAAACGCTGCTAATGCTTTACCTTTTACGGCGTTT
1 AAAAAATGCCGCTATTGCTTTACCTTTTACGGCGTTT
13030 TCTATCCAAA
Statistics
Matches: 99, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
40 66 0.67
41 33 0.33
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Consensus pattern (40 bp):
AAAAAATGCCGCTATTGCTTTACCTTTTACGGCGTTTATG
Found at i:12998 original size:81 final size:82
Alignment explanation
Indices: 12855--13029 Score: 208
Period size: 81 Copynumber: 2.1 Consensus size: 82
12845 TAAAAAAATA
* ** * * *
12855 TTTGCGGCGTTTGTGGAAAAAAACGCTGCTATTGCTTTACCTTTAACGGCGTTTATGAAAAAATG
1 TTTGCGGCGTTTATGGAAAAAAACGCCACTATTACTTTACCTTTAACGGCGTTTACGAAAAAACG
**
12920 CCGCTGTTGCTTTACCT
66 CCGCTAATGCTTTACCT
* * * * *
12937 TTTGCGGCGTTTAT-GAGAAAAATGCCACTATTACTTTACTTTTTACGGCGTTTACGCAAAAACG
1 TTTGCGGCGTTTATGGAAAAAAACGCCACTATTACTTTACCTTTAACGGCGTTTACGAAAAAACG
*
13001 CTGCTAATGCTTTACCT
66 CCGCTAATGCTTTACCT
*
13018 TTTACGGCGTTT
1 TTTGCGGCGTTT
13030 TCTATCCAAA
Statistics
Matches: 78, Mismatches: 15, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
81 65 0.83
82 13 0.17
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.37
Consensus pattern (82 bp):
TTTGCGGCGTTTATGGAAAAAAACGCCACTATTACTTTACCTTTAACGGCGTTTACGAAAAAACG
CCGCTAATGCTTTACCT
Found at i:17050 original size:15 final size:13
Alignment explanation
Indices: 17039--17071 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
17029 GTGTGTGATG
17039 TGAATATATGTGT
1 TGAATATATGTGT
*
17052 TGAATATATG-AT
1 TGAATATATGTGT
17064 TGAATATA
1 TGAATATA
17072 CCTTGTGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.42
Consensus pattern (13 bp):
TGAATATATGTGT
Found at i:17960 original size:13 final size:13
Alignment explanation
Indices: 17937--17989 Score: 61
Period size: 13 Copynumber: 3.9 Consensus size: 13
17927 AATTAAGGCA
*
17937 GTTCACGATAGGG
1 GTTCACCATAGGG
*
17950 GTTCGCCATAGGTG
1 GTTCACCATAGG-G
*
17964 AGTTCACGATAGGG
1 -GTTCACCATAGGG
17978 GTTCACCATAGG
1 GTTCACCATAGG
17990 TGAGTTTGCC
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
13 21 0.64
14 2 0.06
15 10 0.30
ACGTcount: A:0.23, C:0.19, G:0.34, T:0.25
Consensus pattern (13 bp):
GTTCACCATAGGG
Found at i:17976 original size:28 final size:28
Alignment explanation
Indices: 17936--17995 Score: 111
Period size: 28 Copynumber: 2.1 Consensus size: 28
17926 GAATTAAGGC
*
17936 AGTTCACGATAGGGGTTCGCCATAGGTG
1 AGTTCACGATAGGGGTTCACCATAGGTG
17964 AGTTCACGATAGGGGTTCACCATAGGTG
1 AGTTCACGATAGGGGTTCACCATAGGTG
17992 AGTT
1 AGTT
17996 TGCCATAAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.23, C:0.17, G:0.33, T:0.27
Consensus pattern (28 bp):
AGTTCACGATAGGGGTTCACCATAGGTG
Found at i:18007 original size:28 final size:28
Alignment explanation
Indices: 17948--18026 Score: 88
Period size: 28 Copynumber: 2.8 Consensus size: 28
17938 TTCACGATAG
* * * *
17948 GGGTTCGCCATAGGTGAGTTCACGATAG
1 GGGTTCACCATAGGTGAGTTTACCATAA
*
17976 GGGTTCACCATAGGTGAGTTTGCCATAA
1 GGGTTCACCATAGGTGAGTTTACCATAA
*
18004 GGGTT-ACTCATATGTGAGTTTAC
1 GGGTTCAC-CATAGGTGAGTTTAC
18027 TAGACATAGG
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
27 2 0.05
28 41 0.95
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.30
Consensus pattern (28 bp):
GGGTTCACCATAGGTGAGTTTACCATAA
Found at i:22911 original size:164 final size:164
Alignment explanation
Indices: 22501--23967 Score: 1255
Period size: 164 Copynumber: 9.1 Consensus size: 164
22491 CATAAATTAC
* * * * * * * * *
22501 AAGTATTG-TAAAAGATACATAATTTGAAAACCAATTTGCATATTAAAATAAATACAAAATAAGT
1 AAGTATCGTTAAAAGATATATAAATTGAAAACCATTTTACTTATTAAAACAAAAACAAAATAAGC
* * *
22565 ATTTATAATAAAATACG-GGTTTAGGTATAGTAAAAGGTGTATGATTTCAATAACCAAAG-AAAA
66 ATTTATAATAAAATA-GAGGTTTAGGTATAGTGAAAGGTGTATGATTCCGATAACCAAAGCAAAA
* * * * *
22628 TAAGCATTTATAAGACACGATGGAGTATAGA-TTT
130 TAAGCATTTATAAAACACAATGAAATATAAACTTT
* * * *
22662 -AGTCATCGTTAAAAGATATATAATTTGAAAACCATCTTACTTA--ATAATAAAAACAAAATAAG
1 AAGT-ATCGTTAAAAGATATATAAATTGAAAACCATTTTACTTATTAAAACAAAAACAAAATAAG
* * * * * * * *
22724 CATTTATAATAAAATACAAGTTTAAGTATAATAAAAGATGTATGATTCCGATAACGAAAGCGAAA
65 CATTTATAATAAAATAGAGGTTTAGGTATAGTGAAAGGTGTATGATTCCGATAACCAAAGCAAAA
* * *
22789 TAAGAATTTATAAAACACGATGGAATATAAACTTT
130 TAAGCATTTATAAAACACAATGAAATATAAACTTT
22824 AAGTATCGTTAAAAGATATATAAATTGAAAACCATTTTACTTATTAAAACAAAAACAAAATAAGC
1 AAGTATCGTTAAAAGATATATAAATTGAAAACCATTTTACTTATTAAAACAAAAACAAAATAAGC
* * ** * * *
22889 ATTTATAATAAAATATAAGTTTAGGTATAGAAAAAAGTGTACGATTCCGATAACGAAAGCAAAAT
66 ATTTATAATAAAATAGAGGTTTAGGTATAGTGAAAGGTGTATGATTCCGATAACCAAAGCAAAAT
* * *
22954 AAGTATTTATAGAACACAATGGAATATAAACTTT
131 AAGCATTTATAAAACACAATGAAATATAAACTTT
* * * ** *
22988 AGGTATCGTTAAAAGATATATAATTTG-AAACCATTTTGCTTATTAAAACAGGAACAAAATAATC
1 AAGTATCGTTAAAAGATATATAAATTGAAAACCATTTTACTTATTAAAACAAAAACAAAATAAGC
* * * * ** * * * * *
23052 ATTTATAATAAAATACAAGTTTAGGTATTGTAAAAGAAGTA--A----AATAAGCATTTA-TAAC
66 ATTTATAATAAAATAGAGGTTTAGGTATAGTGAAAGGTGTATGATTCCGATAACCA--AAGCAAA
* * ** * * * *
23110 GTACG-ATGAAATATAA-AC-TTTAAATAT---CGTTAA
129 ATAAGCAT-TTATAAAACACAATGAAATATAAAC-TT-T
* *** * * * *
23143 AAGATAT--ATAATTCAT-TAT-AATTCAAAAATCATTATACTTATTAAAATAAAAACAAAAGTA
1 AAG-TATCGTTAAAAGATATATAAATT-GAAAACCATTTTACTTATTAAAACAAAAACAAAA-TA
* * * *
23204 AGCATCTATAATAAAATAGAGGTTTAGGTATAGTGAAAGGTGGATGATTCCGATAACGAAAGAAA
63 AGCATTTATAATAAAATAGAGGTTTAGGTATAGTGAAAGGTGTATGATTCCGATAACCAAAGCAA
**
23269 AATTAA-CATTTATAGTACACAATGAAATATAAACTTT
128 AA-TAAGCATTTATAAAACACAATGAAATATAAACTTT
* * * *
23306 AATTAGTATCGTTAAAAGATATAT-AATTCGAAAACCGTCTTACTTATTAAAATAGAAACAAAAT
1 -A--AGTATCGTTAAAAGATATATAAATT-GAAAACCATTTTACTTATTAAAACAAAAACAAAAT
* * * * *
23370 AAGCATTTATAATAAAATAAAGGTTTAGGTATTGCGGAAGGTGTATGATTCCTATAACCAAAGCA
62 AAGCATTTATAATAAAATAGAGGTTTAGGTATAGTGAAAGGTGTATGATTCCGATAACCAAAGCA
* * ** *
23435 AAATAAGTATTTATATAACACTCGTAAAATATAAACTTT
127 AAATAAGCATTTATAAAACAC-AATGAAATATAAACTTT
* * *
23474 AAGTATCGTTAAAAGATATCTAATTTGAAAACC-TATTTACTTATTGAAACAAAAACAAAATAAG
1 AAGTATCGTTAAAAGATATATAAATTGAAAACCAT-TTTACTTATTAAAACAAAAACAAAATAAG
*
23538 C----ATAATAAAATAGAGGTTTAGGTATAGTGAAAGGTGTATGATTCCGATAACCAAAGAAAAA
65 CATTTATAATAAAATAGAGGTTTAGGTATAGTGAAAGGTGTATGATTCCGATAACCAAAGCAAAA
* *
23599 TAAGCATTTATATAACATCCATG------AAA---T
130 TAAGCATTTATAAAACA-CAATGAAATATAAACTTT
* * * *
23626 -A-TATCGTTAAAAGATATAT-AATTCGAAAATCGTTTTACTTATTAAAACAAAAACAAATTACG
1 AAGTATCGTTAAAAGATATATAAATT-GAAAACCATTTTACTTATTAAAACAAAAACAAAATAAG
* * * *
23688 CATTTATAACAAAATAGAGGTATAGATATGGTGAAAGGTGTATGATTCCGATAACCAAAGCAAAA
65 CATTTATAATAAAATAGAGGTTTAGGTATAGTGAAAGGTGTATGATTCCGATAACCAAAGCAAAA
* * * *
23753 TAAGCATTTATAATATATAATGAAATATAAATTTT
130 TAAGCATTTATAAAACACAATGAAATATAAACTTT
* * * * * *
23788 AAGTATCGTTAAAAGATATAT-AATTCGAAAATCGTTCTACTTATT-AAA-AAAAATAAAGTACG
1 AAGTATCGTTAAAAGATATATAAATT-GAAAACCATTTTACTTATTAAAACAAAAACAAAATAAG
* * *
23850 CATTTATAATAAAATAGAGGTATAGGTATGGTGAAAGGTGTATGATTCTGATAACCAAAGCAAAA
65 CATTTATAATAAAATAGAGGTTTAGGTATAGTGAAAGGTGTATGATTCCGATAACCAAAGCAAAA
* * * *
23915 CAAGCATTTATATAACACTCATAAAATATAAACTTT
130 TAAGCATTTATAAAACAC-AATGAAATATAAACTTT
* * *
23951 AAGCATAGTTGAAAGAT
1 AAGTATCGTTAAAAGAT
23968 GTAGTTTAGG
Statistics
Matches: 1072, Mismatches: 174, Indels: 118
0.79 0.13 0.09
Matches are distributed among these distances:
149 3 0.00
150 50 0.05
151 2 0.00
152 4 0.00
153 7 0.01
154 102 0.10
155 42 0.04
156 9 0.01
157 10 0.01
158 10 0.01
159 5 0.00
160 76 0.07
161 117 0.11
162 165 0.15
163 103 0.10
164 176 0.16
165 56 0.05
166 8 0.01
167 77 0.07
168 50 0.05
ACGTcount: A:0.48, C:0.09, G:0.13, T:0.30
Consensus pattern (164 bp):
AAGTATCGTTAAAAGATATATAAATTGAAAACCATTTTACTTATTAAAACAAAAACAAAATAAGC
ATTTATAATAAAATAGAGGTTTAGGTATAGTGAAAGGTGTATGATTCCGATAACCAAAGCAAAAT
AAGCATTTATAAAACACAATGAAATATAAACTTT
Found at i:24202 original size:29 final size:29
Alignment explanation
Indices: 24160--24218 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
24150 CTAACCAGAA
24160 AGTAAAAGAGGTAGTGAAATTAAATGCTT
1 AGTAAAAGAGGTAGTGAAATTAAATGCTT
24189 AGTAAAAGAGGTAGTGAAATTAAATGCTT
1 AGTAAAAGAGGTAGTGAAATTAAATGCTT
24218 A
1 A
24219 CCAAGAGATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.46, C:0.03, G:0.24, T:0.27
Consensus pattern (29 bp):
AGTAAAAGAGGTAGTGAAATTAAATGCTT
Found at i:30935 original size:41 final size:40
Alignment explanation
Indices: 30833--30989 Score: 190
Period size: 40 Copynumber: 3.9 Consensus size: 40
30823 CGTTTGTGGA
* * *
30833 AAAAAACGCTGCTATTGCTTTACCTTTAACGGCGTTTATG
1 AAAAAATGCCGCTATTGCTTTACCTTTTACGGCGTTTATG
* *
30873 AAAAAATGCCGCTGTTGCTTTACCTTTTGCGGCGTTTATG
1 AAAAAATGCCGCTATTGCTTTACCTTTTACGGCGTTTATG
* * *
30913 AGAAAAATGCCACTATTACTTTA-CTTTTACGGCGTTTACG
1 A-AAAAATGCCGCTATTGCTTTACCTTTTACGGCGTTTATG
* * * *
30953 CAAAAACGCTGCTAATGCTTTACCTTTTACGGCGTTT
1 AAAAAATGCCGCTATTGCTTTACCTTTTACGGCGTTT
30990 TCTATCCAAA
Statistics
Matches: 99, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
39 16 0.16
40 65 0.66
41 18 0.18
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Consensus pattern (40 bp):
AAAAAATGCCGCTATTGCTTTACCTTTTACGGCGTTTATG
Found at i:35010 original size:15 final size:13
Alignment explanation
Indices: 34999--35031 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
34989 GTGTGTGATG
34999 TGAATATATGTGT
1 TGAATATATGTGT
*
35012 TGAATATATG-AT
1 TGAATATATGTGT
35024 TGAATATA
1 TGAATATA
35032 CCTTGTGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.42
Consensus pattern (13 bp):
TGAATATATGTGT
Found at i:35920 original size:13 final size:13
Alignment explanation
Indices: 35897--35949 Score: 61
Period size: 13 Copynumber: 3.9 Consensus size: 13
35887 AATTAAGGCA
*
35897 GTTCACGATAGGG
1 GTTCACCATAGGG
*
35910 GTTCGCCATAGGTG
1 GTTCACCATAGG-G
*
35924 AGTTCACGATAGGG
1 -GTTCACCATAGGG
35938 GTTCACCATAGG
1 GTTCACCATAGG
35950 TGAGTTTGCC
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
13 21 0.64
14 2 0.06
15 10 0.30
ACGTcount: A:0.23, C:0.19, G:0.34, T:0.25
Consensus pattern (13 bp):
GTTCACCATAGGG
Found at i:35936 original size:28 final size:28
Alignment explanation
Indices: 35896--35955 Score: 111
Period size: 28 Copynumber: 2.1 Consensus size: 28
35886 GAATTAAGGC
*
35896 AGTTCACGATAGGGGTTCGCCATAGGTG
1 AGTTCACGATAGGGGTTCACCATAGGTG
35924 AGTTCACGATAGGGGTTCACCATAGGTG
1 AGTTCACGATAGGGGTTCACCATAGGTG
35952 AGTT
1 AGTT
35956 TGCCATAAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.23, C:0.17, G:0.33, T:0.27
Consensus pattern (28 bp):
AGTTCACGATAGGGGTTCACCATAGGTG
Found at i:35967 original size:28 final size:28
Alignment explanation
Indices: 35908--35986 Score: 88
Period size: 28 Copynumber: 2.8 Consensus size: 28
35898 TTCACGATAG
* * * *
35908 GGGTTCGCCATAGGTGAGTTCACGATAG
1 GGGTTCACCATAGGTGAGTTTACCATAA
*
35936 GGGTTCACCATAGGTGAGTTTGCCATAA
1 GGGTTCACCATAGGTGAGTTTACCATAA
*
35964 GGGTT-ACTCATATGTGAGTTTAC
1 GGGTTCAC-CATAGGTGAGTTTAC
35987 TAGACATAGG
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
27 2 0.05
28 41 0.95
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.30
Consensus pattern (28 bp):
GGGTTCACCATAGGTGAGTTTACCATAA
Found at i:41203 original size:164 final size:164
Alignment explanation
Indices: 40793--42259 Score: 1264
Period size: 164 Copynumber: 9.1 Consensus size: 164
40783 CATAAATTAC
* * * * * * * * *
40793 AAGTATTG-TAAAAGATACATAATTTGAAAACCAATTTGCATATTAAAATAAATACAAAATAAGT
1 AAGTATCGTTAAAAGATATATAAATTGAAAACCATTTTACTTATTAAAACAAAAACAAAATAAGC
* * *
40857 ATTTATAATAAAATACG-GGTTTAGGTATAGTAAAAGGTGTATGATTTCAATAACCAAAG-AAAA
66 ATTTATAATAAAATA-GAGGTTTAGGTATAGTGAAAGGTGTATGATTCCGATAACCAAAGCAAAA
* * * * *
40920 TAAGCATTTATAAGACACGATGGAGTATAGA-TTT
130 TAAGCATTTATAAAACACAATGAAATATAAACTTT
* * * *
40954 -AGTCATCGTTAAAAGATATATAATTTGAAAACCATCTTACTTA--ATAATAAAAACAAAATAAG
1 AAGT-ATCGTTAAAAGATATATAAATTGAAAACCATTTTACTTATTAAAACAAAAACAAAATAAG
* * * * * * * *
41016 CATTTATAATAAAATACAAGTTTAAGTATAATAAAAGATGTATGATTCCGATAACGAAAGCGAAA
65 CATTTATAATAAAATAGAGGTTTAGGTATAGTGAAAGGTGTATGATTCCGATAACCAAAGCAAAA
* * *
41081 TAAGAATTTATAAAACACGATGGAATATAAACTTT
130 TAAGCATTTATAAAACACAATGAAATATAAACTTT
41116 AAGTATCGTTAAAAGATATATAAATTGAAAACCATTTTACTTATTAAAACAAAAACAAAATAAGC
1 AAGTATCGTTAAAAGATATATAAATTGAAAACCATTTTACTTATTAAAACAAAAACAAAATAAGC
* * ** * * *
41181 ATTTATAATAAAATATAAGTTTAGGTATAGAAAAAAGTGTACGATTCCGATAACGAAAGCAAAAT
66 ATTTATAATAAAATAGAGGTTTAGGTATAGTGAAAGGTGTATGATTCCGATAACCAAAGCAAAAT
* * *
41246 AAGTATTTATAGAACACAATGGAATATAAACTTT
131 AAGCATTTATAAAACACAATGAAATATAAACTTT
* * * ** *
41280 AGGTATCGTTAAAAGATATATAATTTG-AAACCATTTTGCTTATTAAAACAGGAACAAAATAATC
1 AAGTATCGTTAAAAGATATATAAATTGAAAACCATTTTACTTATTAAAACAAAAACAAAATAAGC
* * * * ** * * * * *
41344 ATTTATAATAAAATACAAGTTTAGGTATTGTAAAAGAAGTA--A----AATAAGCATTTA-TAAC
66 ATTTATAATAAAATAGAGGTTTAGGTATAGTGAAAGGTGTATGATTCCGATAACCA--AAGCAAA
* * ** * * * *
41402 GTACG-ATGAAATATAA-AC-TTTAAATAT---CGTTAA
129 ATAAGCAT-TTATAAAACACAATGAAATATAAAC-TT-T
* *** * * * *
41435 AAGATAT--ATAATTCAT-TAT-AATTCAAAAATCATTATACTTATTAAAATAAAAACAAAAGTA
1 AAG-TATCGTTAAAAGATATATAAATT-GAAAACCATTTTACTTATTAAAACAAAAACAAAA-TA
* * *
41496 AGCATCTATAATAAAATAGAGGTTTAGGTATAGTGAAAGGTGGATGATTCCGATAACGAAAGCAA
63 AGCATTTATAATAAAATAGAGGTTTAGGTATAGTGAAAGGTGTATGATTCCGATAACCAAAGCAA
**
41561 AATTAA-CATTTATAGTACACAATGAAATATAAACTTT
128 AA-TAAGCATTTATAAAACACAATGAAATATAAACTTT
* * * *
41598 AATTAGTATCGTTAAAAGATATAT-AATTCGAAAACCGTCTTACTTATTAAAATAGAAACAAAAT
1 -A--AGTATCGTTAAAAGATATATAAATT-GAAAACCATTTTACTTATTAAAACAAAAACAAAAT
* * * * *
41662 AAGCATTTATAATAAAATAAAGGTTTAGGTATTGCGGAAGGTGTATGATTCCTATAACCAAAGCA
62 AAGCATTTATAATAAAATAGAGGTTTAGGTATAGTGAAAGGTGTATGATTCCGATAACCAAAGCA
* * ** *
41727 AAATAAGTATTTATATAACACTCGTAAAATATAAACTTT
127 AAATAAGCATTTATAAAACAC-AATGAAATATAAACTTT
* * *
41766 AAGTATCGTTAAAAGATATCTAATTTGAAAACC-TATTTACTTATTGAAACAAAAACAAAATAAG
1 AAGTATCGTTAAAAGATATATAAATTGAAAACCAT-TTTACTTATTAAAACAAAAACAAAATAAG
*
41830 C----ATAATAAAATAGAGGTTTAGGTATAGTGAAAGGTGTATGATTCCGATAACCAAAGAAAAA
65 CATTTATAATAAAATAGAGGTTTAGGTATAGTGAAAGGTGTATGATTCCGATAACCAAAGCAAAA
* *
41891 TAAGCATTTATATAACATCCATG------AAA---T
130 TAAGCATTTATAAAACA-CAATGAAATATAAACTTT
* * * *
41918 -A-TATCGTTAAAAGATATAT-AATTCGAAAATCGTTTTACTTATTAAAACAAAAACAAATTACG
1 AAGTATCGTTAAAAGATATATAAATT-GAAAACCATTTTACTTATTAAAACAAAAACAAAATAAG
* * * *
41980 CATTTATAACAAAATAGAGGTATAGATATGGTGAAAGGTGTATGATTCCGATAACCAAAGCAAAA
65 CATTTATAATAAAATAGAGGTTTAGGTATAGTGAAAGGTGTATGATTCCGATAACCAAAGCAAAA
* * * *
42045 TAAGCATTTATAATATATAATGAAATATAAATTTT
130 TAAGCATTTATAAAACACAATGAAATATAAACTTT
* * * * * *
42080 AAGTATCGTTAAAAGATATAT-AATTCGAAAATCGTTCTACTTATT-AAA-AAAAATAAAGTACG
1 AAGTATCGTTAAAAGATATATAAATT-GAAAACCATTTTACTTATTAAAACAAAAACAAAATAAG
* * *
42142 CATTTATAATAAAATAGAGGTATAGGTATGGTGAAAGGTGTATGATTCTGATAACCAAAGCAAAA
65 CATTTATAATAAAATAGAGGTTTAGGTATAGTGAAAGGTGTATGATTCCGATAACCAAAGCAAAA
* * * *
42207 CAAGCATTTATATAACACTCATAAAATATAAACTTT
130 TAAGCATTTATAAAACAC-AATGAAATATAAACTTT
* * *
42243 AAGCATAGTTGAAAGAT
1 AAGTATCGTTAAAAGAT
42260 GTAGTTTAGG
Statistics
Matches: 1073, Mismatches: 173, Indels: 118
0.79 0.13 0.09
Matches are distributed among these distances:
149 3 0.00
150 50 0.05
151 2 0.00
152 4 0.00
153 7 0.01
154 102 0.10
155 42 0.04
156 9 0.01
157 10 0.01
158 10 0.01
159 5 0.00
160 76 0.07
161 117 0.11
162 165 0.15
163 103 0.10
164 176 0.16
165 56 0.05
166 8 0.01
167 78 0.07
168 50 0.05
ACGTcount: A:0.48, C:0.09, G:0.13, T:0.30
Consensus pattern (164 bp):
AAGTATCGTTAAAAGATATATAAATTGAAAACCATTTTACTTATTAAAACAAAAACAAAATAAGC
ATTTATAATAAAATAGAGGTTTAGGTATAGTGAAAGGTGTATGATTCCGATAACCAAAGCAAAAT
AAGCATTTATAAAACACAATGAAATATAAACTTT
Found at i:42494 original size:29 final size:29
Alignment explanation
Indices: 42452--42510 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
42442 CTAACCAGAA
42452 AGTAAAAGAGGTAGTGAAATTAAATGCTT
1 AGTAAAAGAGGTAGTGAAATTAAATGCTT
42481 AGTAAAAGAGGTAGTGAAATTAAATGCTT
1 AGTAAAAGAGGTAGTGAAATTAAATGCTT
42510 A
1 A
42511 CCAAGAGATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.46, C:0.03, G:0.24, T:0.27
Consensus pattern (29 bp):
AGTAAAAGAGGTAGTGAAATTAAATGCTT
Found at i:49225 original size:41 final size:40
Alignment explanation
Indices: 49123--49280 Score: 190
Period size: 40 Copynumber: 3.9 Consensus size: 40
49113 CGTTTGTGGA
* * *
49123 AAAAAACGCTGCTATTGCTTTACCTTTAACGGCGTTTATG
1 AAAAAATGCCGCTATTGCTTTACCTTTTACGGCGTTTATG
* *
49163 AAAAAATGCCGCTGTTGCTTTACCTTTTGCGGCGTTTATG
1 AAAAAATGCCGCTATTGCTTTACCTTTTACGGCGTTTATG
* * * *
49203 AGAAAAATGCCACTATTACTTTACTTTTTACGGCGTTTACG
1 A-AAAAATGCCGCTATTGCTTTACCTTTTACGGCGTTTATG
* * * *
49244 CAAAAACGCTGCTAATGCTTTACCTTTTACGGCGTTT
1 AAAAAATGCCGCTATTGCTTTACCTTTTACGGCGTTT
49281 TCTATCCAAA
Statistics
Matches: 99, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
40 66 0.67
41 33 0.33
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Consensus pattern (40 bp):
AAAAAATGCCGCTATTGCTTTACCTTTTACGGCGTTTATG
Found at i:49249 original size:81 final size:82
Alignment explanation
Indices: 49106--49280 Score: 208
Period size: 81 Copynumber: 2.1 Consensus size: 82
49096 TAAAAAAATA
* ** * * *
49106 TTTGCGGCGTTTGTGGAAAAAAACGCTGCTATTGCTTTACCTTTAACGGCGTTTATGAAAAAATG
1 TTTGCGGCGTTTATGGAAAAAAACGCCACTATTACTTTACCTTTAACGGCGTTTACGAAAAAACG
**
49171 CCGCTGTTGCTTTACCT
66 CCGCTAATGCTTTACCT
* * * * *
49188 TTTGCGGCGTTTAT-GAGAAAAATGCCACTATTACTTTACTTTTTACGGCGTTTACGCAAAAACG
1 TTTGCGGCGTTTATGGAAAAAAACGCCACTATTACTTTACCTTTAACGGCGTTTACGAAAAAACG
*
49252 CTGCTAATGCTTTACCT
66 CCGCTAATGCTTTACCT
*
49269 TTTACGGCGTTT
1 TTTGCGGCGTTT
49281 TCTATCCAAA
Statistics
Matches: 78, Mismatches: 15, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
81 65 0.83
82 13 0.17
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.37
Consensus pattern (82 bp):
TTTGCGGCGTTTATGGAAAAAAACGCCACTATTACTTTACCTTTAACGGCGTTTACGAAAAAACG
CCGCTAATGCTTTACCT
Found at i:53297 original size:15 final size:13
Alignment explanation
Indices: 53286--53318 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
53276 GTGTGTGATG
53286 TGAATATATGTGT
1 TGAATATATGTGT
*
53299 TGAATATATG-AT
1 TGAATATATGTGT
53311 TGAATATA
1 TGAATATA
53319 CCTTGTGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.42
Consensus pattern (13 bp):
TGAATATATGTGT
Done.